In the central Iranian city of Isfahan, Brazilian striker Igor Castro slotted home on the turn in the 16th minute before compatriot and the tournament's top scorer Mota equalised for Pohang with a 56th-minute strike, his 10th goal of the competition.
Mahdi Rajabzadeh blasted the winner from the penalty spot after 74 minutes after Castro had been fouled.
"All Iran was watching us in this match to see what we would do and I'm happy that we were successful," an elated Zobahan coach Mansour Ebrahimzadeh said after the match.
South Korean teams make up half the field in the last eight of Asia's premier club competition but two second half goals ensured Al Shabab have an excellent chance of reducing the K-League contingent after the second leg in Riyadh on Sept. 22.
Midfielder Fahad Hamad found the net for the White Lions from close range after 68 minutes and Uruguayan Juan Manuel Olivera came off the bench to add another with a cool finish in stoppage time.
The victory against the 2006 Asian champions was all the more impressive as the second goal came after Al Shabab midfielder Abdulmalek Al Khaibri had been sent off for a second yellow card.
Seongnam Ilwa's Montenegrin target man Dzenan Radoncic scored twice as the home side drew first blood in the only all-Korean tie of the round with an emphatic 4-1 victory over the Suwon Bluewings.
Radoncic put Seongnam in front after eight minutes before South Korea left-winger Yeom Ki-hun equalised for the Bluewings from a free kick in the 16th.
Former Colombia international Mauricio Molina restored Seongnam's lead just after the half-hour mark with his fifth goal of the competition.
Radoncic added the third with a header midway through the second half before Suwon's Yang Sang-min turned the ball into his own net to round out the scoring eight minutes from time.
Suwon coach Yoon Sung-hyo was unhappy with the playing surface and said: "I don't really want to talk about the game after playing on that kind of pitch, it was nonsense. Even Sunday League players would not want to play on that pitch."
Egged on by their home crowd, Saudi league's most decorated club Al Hilal beat Qatar's Al Gharafa 3-0 in Riyadh.
Mohammed Al Shalhoub opened the scoring in the 13th minute, Ahmed Al Fraidi stretched the lead in the 55th and substitute Waleed Algizani's low shot found the net five minutes from time.
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